I'm not sure if this is a bug or intended. With this code:
mesh_0.setTransparency(255);
mesh_0.setTexture("tex_with_alpha");
mesh_1.setTexture("tex_solid");
Object3D mesh = Object3D.mergeObjects(mesh_0, mesh_1);
Then the mesh_0 part loses the alpha setting (100% transparency --> black).
Sorry if this has been discussed before.
(Tested on Sony Ericsson Xperia Play.)
I believe you need to call "setTransparency;" again on the merged object to say to use the alpha channel.
If you don't want the whole object transparent then you will need to keep them separate.
Transparency is per Object. It's intended and not a bug.